When coming up from Niflheim in the "Mediterranean Sea" level, if you look around there are no other vessels to be seen (apart from Lara's own yacht). However, as soon as Lara climbs back on to her boat, Amanda's tanker is suddenly anchored about half a mile away.
When Lara enters the Croft family crypt, she is already fitted with most of her usual exploring gear, including her guns. However, she still has her secondary weapon and grappling not on her person.
There's a graphical glitch in the Croft Manar level. If you survive the fall on the perimeter of the room where you fight the thralls, you can walk through and off the game graphics.
Lara states that the "Beneath The Ashes" level is a medieval dungeon. In one of the large chambers there is a guillotine, but the guillotine was not invented until the French revolution, well after the end of the medieval era.
After Lara parks her yacht beside Amanda's tanker in the Mediterranean Sea level, if Lara dives in to the water and continues to swim straight down, she will eventually find herself falling out of the sky.